Star Trek: 10 Reasons With Sisko & Kira's Relationship Is Key To Deep Space Nine
9. Learning To Trust
When Sisko arrived on Deep Space Nine, he wasn't sure who he was anymore or how he fit into Starfleet. Wolf 359 was years ago at that point but the event had shaken him. This was due in no small part to the fact that the attack was perpetrated by a high ranking Starfleet officer. Sisko lost his faith in the uniform and didn't know how to trust it.
Kira was in a very similar situation. After finally ousting the Cardassians, many Bajorans felt that asking the Federation for help was just letting another oppressor onto their world. Kira was one of those Bajorans. At the start, the difference between the Federation and the Cardassians was minimal to her.
Through time and cooperation, Kira and Sisko learned to trust each other. The two of them working side by side and being successful at rebuilding Bajor in turn built the trust between the Bajorans and the Federation. Their work slowly quelled the dissenting voices in the new partnership.